Direct sequencing is available only to one group CRUK-CI who have bought their own sequencer. If you know nothing about this, then this page is not for you and you should refer to the Sequencing Only submissions help.

The direct sequencing form is as small as it can be to allow the processing of the run and delivery of correctly processed files. Many of the fields from the SLX submission form are not necessary if you are setting up the sequencer yourself, though the information may need to be supplied on the sequencer itself. Any problems that come up from operating the sequencer incorrectly are, to be blunt, yours!

1. Fill out the SLX identifier which is printed on the tube containing your library (SLX-xxxxx).
2. Select library type from the drop down menu. Some library types have special handling for processing the data, so to get your data easily please pick the correct one. Important: if submitting for the library types “Amplicon low diversity”, “Amplicon high diversity” or “Bisulphite” please read table 3 of the standard sequencing help regarding PhiX spike-in percentage.

1. Complete a separate row with a sample name and index name for each sample within the pool. For example, a pool of six libraries should use six rows.
   1. Sample Name can be anything you choose to represent that sample.
   2. Index must be the corresponding Index Name (e.g. i701_i501) rather than the index sequence. Some index types are grouped (for instance all Nextera kits as they all use the same original set of Illumina Nextera index sequence), so as long as the sequence matches your index sequence you are able to submit using that index name. You do not have to fill in a field to state the index type with direct sequencing: it is determined from the indexes you use in your samples. You cannot mix index types though; all indexes used must be of the same type.
   3. Species is only needed if you have a mix of species in the pool. Use this field to assign a species for any sample whose species differs from that set in cell C11 (the species common across the pool).
2. For a pool with In-Line Barcodes or a pool submitted as index type Unspecified (Other), complete a single row for the whole pool, i.e., a pool of six libraries is still only one row in the sample information table. The index should read “INLINE” for index type “inline barcodes” and “Unspecified Index” if “Unspecified (Other)” has been chosen.